Vader in the Clone wars
by Dark Lord of the X-Men
Summary: What happens when Vader goes back in time to stop the future before it can ever happen? Completely AU, with references to the traditional comics, The Clone Wars TV Series, and KOTOR. Disregards any of Disney's Star Wars mishaps…
1. And so it begins

What happens when Vader goes back in time to stop the future before it can ever happen? Completely AU, with references to the traditional comics and KOTOR. Disregards any of Disney's Star Wars mishaps…

Darth Vader, commander of The Intergalactic Empire's army, stood on the bridge of his flagship, _The Executor,_ overseeing the final stages of his latest and greatest weapon. Sensing the approach of an Imperial officer, the dark lord turned towards him, and silently demanded the reason for the man's intrusion into his personal reverie. The young Coruscanti officer did not fail him.

"Lord Vader! The weapon is almost ready. Within a few hours' time, we can begin our mission…" Pausing, a look of befuddlement passed over they young man's face. "If I may be so bold, M' Lord, what exactly is our mission?"

Even as the words left his mouth, the young man prepared for his rather gruesome end. However, in a completely uncharacteristic moment, Lord Vader simply turned back to his view, leaving the man unscathed. After a moment's pause, Vader spoke.

"To end a war before it has even begun."


	2. Welcome to the Clone Wars

Disclaimer: I do not own Star Wars. If I did, Disney never would have gotten their hands on it...

* * *

Underneath his mask, Lord Vader smiled for the first time in years. His newest project was just completed, and the Emperor was still unaware of his actions. Everything was going according to plan. It was time to begin.

* * *

Storming onto the bridge of _The Executor_ , Darth Vader immediately began issuing orders to the officers and engineers.

"Prepare the engines. Contact the other ships and ensure that everything is prepared. I will accept no failures."

"Yes, Lord Vader!" An older, and high ranked, Moff began issuing orders to the engine crew and communications officers, making sure that the entire armada of 32 Imperial Star destroyers, loaded to the brim with as many Fighters, Ships, Walkers, and troops that they could carry, was fully ready for the challenges that lay ahead of them. _The Executor_ was similarly loaded and prepared, featuring the greatest amount of weapons, supplies, Clone Storm Troopers (far more efficient and accurate than the standard Storm Trooper), and vehicles that any ship in the galaxy had ever seen.

"Sir, the machine will be ready in exactly 10 minutes, 35 seconds."

"Excellent, Commander. Prepare the device for activation."

"Yes, M' Lord!" The same officer as before hurriedly stepped over to a new control panel, and began speaking into comms. and contacting the main control system for the new super weapon.

* * *

Designed to allow transport for even the largest vehicles in the Imperial fleet, the device generated a type of wormhole that would make time travel a reality. With this device Darth Vader planned to lead a massive armada into the past to stop The Intergalactic Empire before it was ever created. The men and women aboard the ships were only informed that they would be going back to help crush the rebellion in its earliest stages, to prevent the massive amounts of death and destruction that would come later, especially with the destruction of DS-1, also known as the Death Star. Only a select few Moffs, Officers and engineers knew the real purpose of the mission.

One such officer, an old and grizzled war veteran, walked up to stand at Vader's left side and oversee the operation.

"M' Lord. The men are ready. The 501'st know the real purpose, but are behind you 110%. They aren't called "Vader's first" for no reason."

"Good." The Dark Lord responded. "They will be an invaluable asset during this fight." Turning to the man standing next to him, Vader continued. "Make sure that the men know what they are going to be fighting. This may open memories for some of the more experienced troopers. Any and all of the troopers with experience in these situations are to be promoted to squad or divisional leaders. Experience and the element of surprise will be two of our greatest weapons.

"Yes, Lord Vader."

"And Rex…"

"Yes, Lord Vader?"

"I am placing you in command of all of the clone troops, as well as the 501'st. Do not fail me."

In a rare show of bravery, at least for the other officers, Rex gave the black cloaked leader a cocky grin and responded "Have I ever?"

* * *

With a sound that reminded many of the ignition of a lightsaber, the giant swirling vortex of a portal opened from its operational base above Raxus Prime.

Vader grinned behind his mask and gave the order to move out. Almost immediately, the massive armada of ships began entering the portal. The voyage, while not long, was bumpy and rough, causing many people to fall over. Vader and Rex, however, appeared completely unfazed by the whole ordeal.

As soon as the shaking stopped, and it took quite a while ( _The Executor_ is indeed a very large ship), Rex began barking orders at the officers aboard the bridge.

"Make shuhr thet all ships got through safely. Remember, we won't be gettin' backup if anyone gets lost…"

As soon as all ships were present and accounted for, the giant portal behind the ships vanished, trapping the Imperials in a new (or is it old?) age.

Turning back to Vader, Rex grinned and said "Welcome beck to the Clone Wars, General."

"This time…" Vader began, staring out the main window of the bridge. "This time, we will do it right. Sidious must die first."

* * *

Two updates in one day! I am on a ROLE! :)

Read and Review PLEASE! I want to know how you all like it.


	3. Jedi Council

Disclaimer: I do not own Star Wars. If I did, Disney never would have gotten their slimy hands on it...

* * *

Anakin Skywalker complained the entire way from his quarters to the Jedi council room.

"Why do I have to be here? It's not like I am a Master…"

"Anakin, why must you complain so? You know how it tires me..." Obi-wan Kenobi groaned, albeit good naturedly.

"Because you drag me to these boring meetings, when I don't even have to be there! I have a padawan now, and I really should be training her."

"Anakin, you know she is presently in classes, and will be so until long after the meeting. You just want to go tinker with your droids…" The bearded Jedi Master grinned at his former apprentice.

"Yes!" The supposed Chosen One admitted, unashamedly. "They are far more interesting than Master Yoda's backwards talk or Master Windu's incessant reminders to be respectful. Honestly, how respectful does he think he is not letting me get a word in edge wise? It's not like I want to be at these meetings…" While unbecoming of the Jedi knight, it was not uncommon to see him pouting about the temple. This, was one of those times.

"Anakin! Stop pouting like some youngling who didn't get pudding for dinner! If you ever want to amount to anything in this order, you will learn to sit through the meetings, and pay attention! Maybe you will get lucky and offer some helpful piece of advice."

"Yeah, right! Like that will ever happen!"

"Actually, Anakin, Master Yoda asked for you personally. It seems that, with the war and all, our fighters are quickly becoming obsolete, and Grievous and Dooku are only getting better and better technology. Master Yoda, in his backwards talk,…" The older Jedi teased his former apprentice, who started to go red in the face, "asked for you specifically. Despite your tendency to crash your ships, you are one of the best pilots we have. He thought that you input would be invaluable in choosing some new fighters."

"Finally! Something I can actually do!" Anakin cheered, as they entered the council chamber, only to notice that all of the others were already seated and waiting for the "Silver-tongued negotiator" and "the hero without fear".

"That indeed is a rarity." Master Windu's voice dripped with sarcasm. "You're late."

"As always…" Jedi Master Ki-Adi Mundi mumbled underneath his breath, but loud enough that most of the room still heard him… and agreed…

Kenobi took his seat in the circle, while Anakin stood next to him master's seat, since he did not have a seat of his own.

"New surprises, this war brings" The little green Jedi Grand Master Yoda began the meeting.

"Indeed," Jedi Master Plo Koon responded, calling up a holographic map that quickly filled the room. "The Seperatists are being forced back towards the outer rim, but are advancing towards Naboo. It seems that we are only trading planets."

"There was a disturbance detected near Raxus Prime," Jedi Master Ki-Adi Mundi replied, gesturing towards a blip on the holographic map. "Apparently a large group of ships exited some sort of portal above the planet. We believe it might be a Seperatist armada looking to launch a massive campaign in that area."

"Isn't Raxus Prime the junk planet?" Jedi Master Kit Fisto asked, unsure if he was remembering planets correctly.

"Yes," Anakin replied, thinking. "Could the Seperatists be looking to take junk droids in order to melt them down to form new armies or ships?"

"Logical, that would be." Master Yoda acknowledged Skywalker actually making a useful contribution to one of their meetings.

"We cannot let that happen." Mace Windu responded with a look of serious determination on his face. "Skywalker, Kenobi. Take 2 legions of clones and several cruisers. Try to prevent them from taking control of the planet. Those are resources that the seperatists need vitally, and could have a massive impact on the result of the war."

"Consider it done, Master." Kenobi replied diplomatically.

"To another point, this bring us." Yoda began. "Becoming out-classed, our Starfighters are. Called Skywalker here to help us, I have. Make a decision, we must. New fighters, the order needs."

"I cannot agree more." Jedi Master Luminara Unduli responded. "our Delta-7's are no longer an edge in this war."

There were murmurs of consent all around the council chamber.

"Chose, we must. What kind of Starfighter, we need?" Yoda asked the other masters, and Anakin.

"It must be fast and nimble." Jedi Master Plo Koon responded. An ace pilot himself, Plo Koon knew the benefits of having a ship that could easily out-manoeuvre the competition.

"However, it must have good armour." Responded Kit Fisto. Although a half decent pilot, Fisto preferred fighting on land or in the water to fighting in space, a sentiment that Kenobi could agree with.

"Masters, may I suggest the Eta-2?" At the looks of befuddlement on the faces of the council, Anakin sighed and pulled up an image of the Starfighter in question for the council to see. "The Eta-2 Actis-class interceptor. Smaller than the Delta-7 and the Delta-7B, this ship has an actual astromech droid socket, meaning that you can fit an entire astromech droid rather than a truncated version."

"Can't the Delta-7B do that too?" Ki-Adi Mundi asked.

"Yes, but the 7B is much larger that the Eta-2."

* * *

Three hours later, the meeting was finally finished, with the Jedi Council agreeing to take Skywalker's suggestion and begin purchasing the Eta-2 Starfighter.

"Obi-Wan! I'm going to grab Ahsoka and tell her that we have a mission to go to. I'll meet you in the hangar in 1 hour!"

"Anakin! Wait! That's why we have comlinks!" Kenobi's words, however, fell on deaf ears, as his former apprentice went to chase down his own apprentice.

"Some things never change." Kenobi turned around to see Jedi Master Shaak Ti walking towards him, laughing.

"Yes. It seems like just yesterday I was trying to stop a much younger Anakin from running the in the temple because he wanted to go work on some of the broken droids…" Obi-wan chuckled, remembering times that didn't seem so long ago.

"Well, I suppose I should leave you to get ready for your mission. Make sure to take an extra lightsaber. One of you always seems to lose theirs. Oh, and don't get shot."

"An unfortunate habit." Kenobi grinned. "I'll try to remember your advice."

* * *

Three days later, the small republic fleet came out of lightspeed to see something that they never expected. A massive armada had surrounded Raxus Prime, and were quickly taking control of it, building new ship yards and other facilities.

Quickly, Commander Cody, who was aboard the bridge at the time that they dropped out of hyper-space, commed his Jedi General.

"General Kenobi… You are going to want to see this…"


	4. Discoveries

HOLY TOMATO SAUCE! How long has it been since I last updated? Even I have lost track! Thank you to my loyal readers that are sticking with me. Well, here is a consolation prize.

Thank you to the guests that reviewed Chapter 3:

To the Guest who left 2 reviews about ideas and information: Thank you for pointing that out about the executor, although that is why Raxus Prime was targeted first. There are a LOT of resources and equipment there that can be either retrofitted, or reformed to fit the needs of Vader and the Storm Troopers. Likewise, Rex is going to push for an overhaul of the storm trooper armor. We might see something similar to the First Order Storm Troopers (since that armor was the only good thing, besides Vader's helmet, to come out of Disney's massacre of the Star Wars Universe).

To the other Guest who requested having an AnaSoka relationship (Anakin/Ahsoka), Sorry. Anakin is still going to be with Padme, and the twins will still be coming (eventually). But Vader on the other hand…

Disclaimer: I do not own Star Wars. If I did, Disney never would have gotten their slimy hands on her…

* * *

Kenobi raced up to the bridge, Anakin and Ahsoka following not far behind him.

"Did Cody say what was going on?" Anakin asked, worried.

"Not really. He said that there was another fleet surrounding Raxus Prime."

"Droids?" Ahsoka asked, a look of befuddlement starting to cover her face.

"No. He said he didn't recognise it." Kenobi responded, before doubling his speed for the final stretch to reach the bridge.

"Cody! What happened?" Obi-wan asked as he screeched to a halt next to the clone commander.

"Why don't you see for yourself?" Cody responded, gesturing to the large windows that dominated the walls of the Venator-class cruiser.

The junk planet was almost completely surrounded by a nearly impenetrable wall of unknown cruisers, vaguely resembling the very ship that the Jedi were presently on.

"Force! That's a LOT of ships!" Ahsoka exclaimed, her jaw dropping at the mere sight of the armada that had amassed itself around the planet.

"They certainly aren't separatists, unless these are a new breed. They almost look like our ships, but a lot more advanced." Anakin spoke, trying to analyze the other ships.

At that moment, all the coms on the Republic ships activated, showing Darth Vader, in all of his black-cloaked glory. Before the shocked Republic forces could respond, Vader began to speak.

"Soldiers of the republic! I am Darth Vader, commander-in-chief of the new Galactic Empire, and Dark Lord of the Sith. I am here to liberate those oppressed by the Separatists, and enlighten those that are blinded by the Republic's idiocrasy. For those officers who wish to fight for a cause worth living for, I extend an invitation to join my fleet and officers. And to the Clones who fight so diligently under their Jedi Generals, but are brushed off and disregarded by them, I invite you to join my forces. You will be treated with respect, as an equal. No one person is more important than another. If 1 part was missing from a machine, that machine would not function. No part is more important than another, and no soldier is more important than his brother. You have 5 minutes to make a decision, before we will be forced to assume you are all enemies. I will re-establish contact in that time to arrange for those who wish to be respected and honoured for their sacrifice to be transferred to an army that will appreciate them.

"Do NOT try to run. Your ships systems are being jammed, and are inoperable." With those departing words, the image of the new Sith Lord disappeared, leaving bewilderment and questioning to run rampant amongst the Republic forces.

* * *

Aboard Vader's Imperial ships, Vader himself ended his message, and crews immediately began bustling around him to prepare scripted messages with which to greet newcomers to the Imperial ships, as well as the contact which Vader would soon make.

"DIdn' know you could speak loike that, General." Rex mused, a look of contemplation on his face.

"As much as I am loathe to admit it, Kenobi did have some good attributes that may have rubbed off on me." If one could see within the helmet of the black monolith that is Darth Vader, they would have noticed the slight tainting of an embarrassed blush staining the scarred and burnt cheeks of the Dark Lord.

"Well, every good emperor is going to have to make speeches. You won't be an exception."

"That may be so, but I am still a man of action. I prefer to fight rather than talk." The Dark Lord responded, his 1 pointed finger driving the point and silently threatening anyone who inferred otherwise.

"No arguments there. It must be why we get along so well." The aged Clone Commander smirked, responding to the new "Galactic Emperor."

* * *

Aboard the Republic ships, there was a flurry of activity and chatter. While many of the officers had volunteered to join the fight, moral was low amidst the republic navy. Likewise, a large portion of the clones and junior officers that ran the ships were highly considering accepting Darth Vader's offer. They did not always have the benefit of working with officers and generals that truly appreciated them like General Skywalker or General Kenobi. Many of them felt wronged and even abused by their Jedi and Military leaders.

"Captain, what's going on?" Kenobi yelled over the din of squabble, chatter, and barked orders in the Command Bridge of the Cruiser.

"We can't move! All engines are down, comms have been disabled, and sensors are being jammed! We are totally immobile!" The uniformed Captain of the ship yelled back, the din in the room growing louder by the second.

"What about fighters? Can we get defenses up? Can we get transports away?" Anakin bellowed back, trying to find a way around the present predicament.

"Internal communications reports no issues with the hangers. Should we scramble fighters?" A junior officer manning the internal communication booth reports back.

Before the Captain could even reply, Skywalker barked out "SCRAMBLE! Open the hangar bay doors, but DO NOT LAUNCH! He said that we have 5 minutes to respond. Master! You have less than 5 minutes to come up with a response."

"He's asking for us to 'join or die'! How do we respond to that!?" Ahsoka interrupted.

"Very carefully." Kenobi responded with a wry grin the showed little humour.

* * *

"M'Lord!" An Imperial Officer rushed up to Darth Vader and Captain Rex, who were still looking out the main viewport, and offered a quick salute. "We are receiving an incoming transmission from Admiral Granger of the _ISD Rampage_. He asked to speak with you."

Without a word, the black armoured behemoth turned and stalked over to the large view-screen meant for conversing between the ships of the fleet.

"Lord Vader! What is the meaning of this? Those are Republic Cruisers! They were all decommissioned and destroyed YEARS ago!" The overweight, pompous Admiral began barking even before Vader had fully entered the visibility area of the view screen.

"Correct, Admiral. They are indeed Republic Cruisers. Your observational skills are impeccable." Lord Vader drawled, intentionally demeaning the senior officer of the _Rampage_.

"Are the rebels fighting with Venator cruisers now? How did they even obtain such artifacts? You were supposed to have overseen the destruction of those relics!" Granger continued on, hardly noticing that Vader had even responded to him. A fatal mistake for any imperial officer.

His dark presence roiling, making even non-force sensitives aware of the nigh-unbridled rage bubbling within the obsidian mask, Vader glared at the belligerent Admiral on the other end of the line, who was only now beginning to realize that he might have made a critical mistake.

"Unless you miraculously gained a few thousand IQ points, ADMIRAL," The title dripped out of his mask, covered in venom and sarcasm. "… you may not have noticed that we have just passed through a worm-hole to send us back in time. We have just gone 20 years into the past, to the height of the Clone Wars. Thus, we are expecting to see and fight Venator class Republic Ships. If you had bothered to pay attention to the MASS COMMUNIQUE I just issued, you would have noticed that I addressed those ships PERSONALLY! However, your foolishness and insolence have blinded you. You have failed me for the last time." With those infamous words, Admiral Granger's hands leapt to his throat, where he could already feel the invisible pressure that had been the end of thousands of Imperial officers that had failed to impress Lord Vader, or even complete their job with some degree of competency. With a strangled cry, followed by a gurgle, Admiral Granger's feet left the deck, even as the eyes of everyone present aboard the bridge of the _Rampage_ turned to watch the final moments of their senior officer. With a brutal crack, and a thud of a body hitting the floor, Admiral Jant Granger's reign of foolishness was brought to an end.

"Somebody remove that waste of space." Vader continued speaking to the bridge crew aboard the _Rampage_. "Who is the next most senior officer aboard your ship?"

A startled lieutenant who had accidentally wandered into view of Lord Vader's transmission stammered out, "My LORD! Uh… uh… the m-m-most senior Naval officer w-w-w-would be…"

"NO, lieutenant, I asked who the most senior OFFICER was, not just Naval." Vader corrected, feeling his anger beginning to ebb again.

"That would be me, SIR!" A middle-aged officer stepped into view of the screen. "Colonel Maximilian M. Veers, SIR!" Dressed in the typical green uniform denoting the Military and its personnel, Colonel Veers stood an impressive 6 feet 4 inches tall, and built like a AT-AT, almost matching Lord Vader himself in size.

"Colonel Veers, you are now in charge of the ship. I will have a COMPETENT naval officer transferred to the _Rampage_ immediately." Vader ordered, informing a "Ground-Pounder" that he was now in charge of his "Mother-ship".

"With all due respect My Lord, why me? Why not place the second-in-command of the ship in charge? Surely, they would know the personnel and naval combat tactics better than I." Veers asked.

"Simple," Vader responded. "I don't trust anyone trained under that buffoon to be half-way competent at their job. I pray that you will not follow in their footsteps, Veers." Vader responded, finger threatening the military commander even through their comms.

"Of course not, SIR!" Veers snapped to attention and saluted his commander in chief.

"Very good, Veers. Perform competently, and I may see you transferred to _The Executor_. Your record is impressive, even by my standards." Vader responded, dropping a complement that astounded everyone who heard, including the behemoth of a Colonel.

"Thank you, SIR! It will be done, SIR!" Veers saluted again, pride blooming in his chest. He was instantly determined to do the best job possible.

Without another word, Vader ended the transmission to the _Rampage_ and turned to the young face currently inhabiting his communication array.

"Lieutenant…"

"Krennic, M'Lord. Nephew of former Director Krennic of the ISB" The Lieutenant responded proudly, his knees quaking slightly, but determined to make a good impression on his commander.

"I care not for pedigrees and connections, lieutenant. Your only saving grace might be that you perform your duties competently and efficiently." Vader warned, his black-gloved finger waving less than an inch from the young man's face.

"Of Course, M'Lord." The man swallowed, his knees shaking more visibly now.

"Contact the _Chimaera_ , and have them transfer Captain Thrawn to the _Rampage_. I want to be assured that they will perform properly." Vader ordered, turning away from the communications pit.

"That alien? Whatever for?" Young Krennic snorted, disgusted with the mere thought of the Chiss Officer.

The entire bridge of the _Executor_ became silent, waiting for the impending doom of the young man. Lord Vader slowly turned, anger blazing through the ebony mask before he began to stalk towards the insolent officer. Krennic froze, fear plainly visible in his eyes as the black behemoth bore down on him, promising no mercy for questioning his orders or reasoning.

Both, however, were distracted by the second officer at the station quickly turning back to his station and repeating "Contacting _Chimaera_ , aye Sir."

Lord Vader's head swiveled to gaze upon the back of the second-lieutenant who was also at the communications controls. Before Vader even had a chance to speak, the lieutenant had finished opening communications with the aforementioned ship. Giving a snappy salute, the uniformed anomaly quickly informed the communications officers aboard the ISD _Chimaera_ that their Captain was about to be transferred, under Lord Vader's orders, to the _Rampage_ , and to make it quick. As soon as the transmission was complete, and the _Chimaera_ had confirmed receipt of the orders, the officer turned around and, saluting Darth Vader, informed him "The _Chimaera_ will be transferring Captain Thrawn to the ISD _Rampage_ ASAP."

It took a moment before even Vader responded, saying "Very good, lieutenant. Carry on." With that, Darth Vader returned to his spot next to an amused looking Captain Rex, and a terrified Lieutenant Krennic slumped to the floor, his knees finally giving out on him. His comrade stooped down to help pick him up, and dropped him unceremoniously into the chair at his station.

Responding to the unspoken question in his teammate's eyes, the other Lieutenant shrugged and said "I started serving the Axxilan Anti-Pirate fleet. To survive there, you have to know how to keep a cool head and stay focused in dangerous circumstances, especially when the pirates have you out-manned, out-gunned, and out-run."

Glancing quickly back at the now blinking console, he yelled out, "LORD VADER! Incoming transmission from the Republic Ship! Transferring to the primary viewscreen now."

Rex glanced over at his commander and muttered "it's only been 3 minutes. They're early…"

Vader stormed over to the viewscreen, the same one from which he killed Admiral Granger not 1 minute prior. Almost as soon as he had stopped, the transmission blinked to life, showing several faces, including several that haunted him to this day. The temperature in the bridge of the _Executor_ plummeted several degrees as the Sith Lord growled out, "KENOBI!..."

* * *

Bonus points if you can tell me who the second Comms Officer is. :)

Hopefully, it won't be another freaking YEAR before I update this again...


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